rs6857726

Homo sapiens
C>A / C>T
COL25A1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0220 (6594/29896,GnomAD)
A=0182 (5315/29118,TOPMED)
A=0201 (1005/5008,1000G)
A=0234 (903/3854,ALSPAC)
A=0233 (863/3708,TWINSUK)
chr4:109273128 (GRCh38.p7) (4q25)
AD
GWASdb2
1   publication(s)
See rs on genome
43 Enhancers around
28 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.109273128C>A
GRCh38.p7 chr 4NC_000004.12:g.109273128C>T
GRCh37.p13 chr 4NC_000004.11:g.110194284C>A
GRCh37.p13 chr 4NC_000004.11:g.110194284C>T

Gene: COL25A1, collagen type XXV alpha 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
COL25A1 transcript variant 3NM_001256074.1:c.N/AIntron Variant
COL25A1 transcript variant 2NM_032518.2:c.N/AIntron Variant
COL25A1 transcript variant 1NM_198721.3:c.N/AIntron Variant
COL25A1 transcript variant 4NR_045756.2:n.N/AIntron Variant
COL25A1 transcript variant X1XM_011532333.2:c.N/AIntron Variant
COL25A1 transcript variant X2XM_011532334.2:c.N/AIntron Variant
COL25A1 transcript variant X3XM_011532335.2:c.N/AIntron Variant
COL25A1 transcript variant X4XM_011532338.2:c.N/AIntron Variant
COL25A1 transcript variant X5XM_017008735.1:c.N/AIntron Variant
COL25A1 transcript variant X6XM_017008736.1:c.N/AIntron Variant
COL25A1 transcript variant X7XM_011532355.2:c.N/AGenic Upstream Transcript Variant
COL25A1 transcript variant X9XM_011532356.2:c.N/AGenic Upstream Transcript Variant
COL25A1 transcript variant X10XM_011532358.2:c.N/AGenic Upstream Transcript Variant
COL25A1 transcript variant X8XM_017008737.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.931A=0.069
1000GenomesAmericanSub694C=0.690A=0.310
1000GenomesEast AsianSub1008C=0.763A=0.237
1000GenomesEuropeSub1006C=0.765A=0.235
1000GenomesGlobalStudy-wide5008C=0.799A=0.201
1000GenomesSouth AsianSub978C=0.770A=0.230
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.766A=0.234
The Genome Aggregation DatabaseAfricanSub8694C=0.886T=0.000
The Genome Aggregation DatabaseAmericanSub834C=0.650T=0.00,
The Genome Aggregation DatabaseEast AsianSub1610C=0.765T=0.000
The Genome Aggregation DatabaseEuropeSub18456C=0.738T=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29896C=0.779T=0.000
The Genome Aggregation DatabaseOtherSub302C=0.660T=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.817A=0.182
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.767A=0.233
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs68577260.000973alcohol dependence21314694

eQTL of rs6857726 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs6857726 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr4113242914113243330E067-2920
chr4113261173113261262E07014923
chr4113261322113261490E07015072
chr4113261873113261954E07015623
chr4113262022113262597E07015772
chr4113262022113262597E07115772
chr4113242914113243330E072-2920
chr4113249106113249457E0722856
chr4113249469113249549E0743219
chr4113204233113204301E081-41949
chr4113204401113204441E081-41809
chr4113204483113204557E081-41693
chr4113204589113204643E081-41607
chr4113204847113204892E081-41358
chr4113246803113246983E081553
chr4113249106113249457E0812856
chr4113260938113261017E08114688
chr4113261173113261262E08114923
chr4113261322113261490E08115072
chr4113261873113261954E08115623
chr4113262022113262597E08115772
chr4113263082113263528E08116832
chr4113264204113264396E08117954
chr4113264422113264472E08118172
chr4113264569113265556E08118319
chr4113266522113266572E08120272
chr4113269250113269384E08123000
chr4113269494113270238E08123244
chr4113272148113272198E08125898
chr4113249106113249457E0822856
chr4113249469113249549E0823219
chr4113260829113260891E08214579
chr4113260938113261017E08214688
chr4113261873113261954E08215623
chr4113262022113262597E08215772
chr4113262667113262721E08216417
chr4113263082113263528E08216832
chr4113264204113264396E08217954
chr4113264422113264472E08218172
chr4113264569113265556E08218319
chr4113266522113266572E08220272
chr4113269250113269384E08223000
chr4113269494113270238E08223244







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr4113205214113205682E067-40568
chr4113205812113207748E067-38502
chr4113230382113230665E067-15585
chr4113205214113205682E068-40568
chr4113205812113207748E068-38502
chr4113218051113219505E068-26745
chr4113230382113230665E068-15585
chr4113205214113205682E069-40568
chr4113205812113207748E069-38502
chr4113218051113219505E069-26745
chr4113230382113230665E069-15585
chr4113205214113205682E070-40568
chr4113205812113207748E070-38502
chr4113205214113205682E071-40568
chr4113205812113207748E071-38502
chr4113218051113219505E071-26745
chr4113230382113230665E071-15585
chr4113205214113205682E072-40568
chr4113205812113207748E072-38502
chr4113205812113207748E073-38502
chr4113230382113230665E073-15585
chr4113205214113205682E074-40568
chr4113205812113207748E074-38502
chr4113218051113219505E074-26745
chr4113205812113207748E081-38502
chr4113205214113205682E082-40568
chr4113205812113207748E082-38502
chr4113230382113230665E082-15585